Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2258 to 2307 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		network_comparison
    		green
    1129 m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] CDC25A Subtracted 258.558 5.642 252.916
    1130 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] PA2G4 Divided 221.285 1.02732 215.4
    steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA Subtracted 187.022 5.631 181.391
    1131 transducin-like enhancer protein 4. [swissprot;acc:q04727] TLE4 219.438 5.62 213.818
    vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] no value Divided 218.484 1.02731 212.675
    1132 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] API5
    folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] FPGS Subtracted 225.906 5.618 231.524
    1133 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] no value 204.404 210.022
    sec13-related protein. [swissprot;acc:p55735] SEC13 Divided 218.484 1.02731 212.675
    1134 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] TLE3 Subtracted 219.401 5.616 213.785
    vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] ATP6V1G3 Divided 218.484 1.02731 212.675
    1135 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] EN2 Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] ATP6V1B2 Divided 218.484 1.02731 212.675
    1136 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] CXXC1 Subtracted 219.399 5.615 213.784
    yeast sec31p homolog. [refseq;acc:nm_014933] SEC31A Divided 218.484 1.02731 212.675
    1137 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] ABT1 Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] ATP6V1G1 Divided 218.484 1.02731 212.675
    1138 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] no value Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] ATP6V1E1 Divided 218.484 1.02731 212.675
    1139 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] GDAP1L1
    transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] TLE2 Subtracted 219.374 5.615 213.759
    1140 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] DDX39 Divided 218.484 1.02731 212.675
    hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] HECW1 Subtracted 219.399 5.615 213.784
    1141 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] GDAP1 Divided 218.484 1.02731 212.675
    transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] no value Subtracted 219.375 5.608 213.767
    1142 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] GIT1 216.729 5.605 222.334
    vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] ATP6V1D Divided 218.484 1.02731 212.675
    1143 kinesin protein. [refseq;acc:nm_032559] KIF2B Subtracted 224.858 5.594 219.264
    secretory pathway component sec31b-1. [refseq;acc:nm_015490] SEC31B Divided 218.484 1.02731 212.675
    1144 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 Subtracted 135.844 5.585 130.259
    vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] ATP6V1H Divided 218.484 1.02731 212.675
    1145 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] KIF21A Subtracted 224.805 5.554 219.251
    vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] ATP6V1F Divided 218.481 1.0273 212.675
    1146 ubiquitin. [swissprot;acc:p02248] no value Subtracted 209.061 5.543 203.518
    vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] ATP6V1B1 Divided 218.483 1.0273 212.676
    1147 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] PEX14 208.651 1.02729 203.109
    Subtracted 5.542
    1148 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] no value 224.878 5.536 219.342
    ubiquitin. [swissprot;acc:p02248] Divided 209.061 1.02724 203.518
    1149 bystin. [swissprot;acc:q13895] BYSL 239.505 1.0271 233.185
    kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] KIF2A Subtracted 224.764 5.523 219.241
    1150 sorting nexin 1. [swissprot;acc:q13596] SNX1 Divided 209.868 1.02694 215.522
    vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] ATP6V0C Subtracted 218.186 5.514 212.672
    1151 metaxin 1. [swissprot;acc:q13505] MTX1 Divided 199.552 1.02693 204.925
    sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] SGCZ Subtracted 218.186 5.514 212.672
    1152 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] EPS8L1 Divided 221.939 1.02682 216.143
    golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] ACBD3 Subtracted 218.186 5.514 212.672
    1153 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] SGCD
    epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] EPS8 Divided 221.93 1.02676 216.146
    1154 cellular modulator of immune recognition. [refseq;acc:nm_145021] MARCH8 Subtracted 218.186 5.514 212.672

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/